(#include "martini_v2.0_ions.itp") is shown in the system.top file. However, I found out that the above two lines could still work after removing the (#include "martini_v2.0_ions.itp"). Also, I can change "NA" and "CL" to any other names without any errors.

So how the CG ions are reflected in the CG system? I think the CG ions are different from the all-atom ions, right?

Gromacs doesn't use martini_v2.0_ions.itp until you grompp the output of the 2nd line again for your minimization run. If you remove this line, if you don't have the file present in the directory, or have strange atom names, it will complain at the first of these two steps.

However, in the "system_genion.gro" file, it is shown as:
61326NA+NA70524 2.333 1.929 2.965
My understanding is, this means the residue name is "NA+" while the atom name is "NA". So why the atom name is "NA" instead of "NA+"?

Hi Cheng, yeah I know that happens, you can safely ignore the difference warnings in this case grompp - maxwarn 1or you can do what you did without problems. I personally prefer your solution, because on the end gromacs will take the names from the top file and NA is just a little more convenient to work with on the future than NA+ e.g. in selecting for visualization.